Pop Sci

llm_microbial genetics_and_function

The chromatin landscape of the histone-possessing Bacteriovorax bacteria [RESEARCH]
Unveiling Hidden Microbial Diversity in Mars2020 Mission Assembly Cleanrooms withMolecular Insights into the Persistent andPerseverance of Novel Species DefyingMetagenome Sequencing
Molecular Requirements for C. elegans Transgenerational Epigenetic Inheritance of Pathogen Avoidance
Towards a monograph of marine Verrucariaceae in Southern South America and maritime Antarctica: Integrative taxonomy reveals a previously unknown diversity
The Type IV Secretion System of Patescibacteria is homologous to the bacterial monoderm conjugation machinery
Genome-wide identification of genes involved in beetle odoriferous defensive stink gland function recognizes Laccase2 as the phenoloxidase responsible for toxic para-benzoquinone synthesis
Impact of natural transformation on the acquisition of novel genes in bacteria
Differential expression of transposable elements and upregulation of nucleic acid sensing pathways in pterygium
Inflammation switches the chemoattractant requirements for naive lymphocyte entry into lymph nodes
Evolutionary study and structural basis of proton sensing by Mus GPR4 and Xenopus GPR4
Cervicovaginal microbiome and natural history of Chlamydia trachomatis in adolescents and young women
A pair of LysM receptors mediates symbiosis and immunity discrimination in Marchantia
Genes, Vol. 16, Pages 89: Genome Sequencing Reveals the Potential of Enterobacter sp. Strain UNJFSC003 for Hydrocarbon Bioremediation
Genes, Vol. 16, Pages 156: Transcriptomic Characterization of miRNAs in Apis cerana Larvae Responding to Ascosphaera apis Infection
Genes, Vol. 16, Pages 170: Long Noncoding RNAs Responding to Ethanol Stress in Yeast Seem Associated with Protein Synthesis and Membrane Integrity

llm_dna_binding factors_and_chromatin_regulation

KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome [METHODS]
Analysis of a cell-free DNA-based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations [RESEARCH]
ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens
Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers
Inhibition of HMGA2 binding to AT-rich DNA by its negatively charged C-terminus
Contribution of DNA breathing to physical interactions with transcription factors
Genome-wide exploration of the transcriptional regulatory landscape in the early-diverging fungus R. microsporus reveals pervasive DNA methyl adenine regulatory network
Structural determinants of co-translational protein complex assembly
A biophysical basis for the spreading behavior and limited diffusion of Xist
An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development
Centromeric chromatin clearings demarcate the site of kinetochore formation
Ligand interaction landscape of transcription factors and essential enzymes in E. coli
Chaperoning RNA into granules

llm_single cell_sequencing_methods

Inferring disease progression stages in single-cell transcriptomics using a weakly supervised deep learning approach [METHODS]
A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples [METHODS]
Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning
Genetic deconvolution of embryonic and maternal cell-free DNA in spent culture medium of human preimplantation embryos through deep learning
CANDI: self-supervised, confidence-aware denoising imputation of genomic data
CellPhenoX: An eXplainable Cell-specific machine learning method to predict clinical Phenotypes using single-cell multi-omics
Evaluation of out-of-distribution detection methods for data shifts in single-cell transcriptomics
Estimating the effect of tissue- and blood-derived cell reference matrices on deconvolving bulk transcriptomic datasets
ECLARE: multi-teacher contrastive learning via ensemble distillation for diagonal integration of single-cell multi-omic data
Integrating bulk and single cell RNA-seq refines transcriptomic profiles of individual C. elegans neurons
The disparities and development trajectories of nations in achieving the sustainable development goals
High-rate quantum LDPC codes for long-range-connected neutral atom registers
Real-time mirroring of therapy
A deep learning pipeline for three-dimensional brain-wide mapping of local neuronal ensembles in teravoxel light-sheet microscopy

llm_role_of genes_in_tumor_progression

Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression [METHODS]
Methyl-dependent auto-regulation of the DNA N6-adenine methyltransferase AMT1 in the unicellular eukaryote Tetrahymena thermophila
Fam170a deficiency causes male infertility by impairing histone-to-protamine exchange during mouse spermiogenesis
Auto-methylation of the histone methyltransferase SetDB1 at its histone-mimic motifs ensures the spreading and maintenance of heterochromatin
Strain background interacts with chromosome 7 aneuploidy to determine commensal and virulence phenotypes in Candida albicans
Epigenetic priming promotes acquisition of tyrosine kinase inhibitor resistance and oncogene amplification in human lung cancer
Ectopic expression of DNMT3L in human trophoblast stem cells restores features of the placental methylome
Pan-cancer analysis of biallelic inactivation in tumor suppressor genes identifies KEAP1 zygosity as a predictive biomarker in lung cancer
Fine-tuning of gene expression through the Mettl3-Mettl14-Dnmt1 axis controls ESC differentiation
KDM6B-dependent epigenetic programming of uterine fibroblasts in early pregnancy regulates parturition timing in mice
Genes, Vol. 16, Pages 75: The X-Linked Tumor Suppressor TSPX Regulates Genes Involved in the EGFR Signaling Pathway and Cell Viability to Suppress Lung Adenocarcinoma
Genes, Vol. 16, Pages 112: Functional Testing of ETV6 Variants: Is the Evaluation of Their Intracellular Localization Sufficient in Assessing Pathogenicity?
Genes, Vol. 16, Pages 128: The Impact of Klotho in Cancer: From Development and Progression to Therapeutic Potential
Genes, Vol. 16, Pages 133: Exploring miR-21 Knock-Out Using CRISPR/Cas as a Treatment for Lung Cancer
Genes, Vol. 16, Pages 138: Combined Effect of Conventional Chemotherapy with Epigenetic Modulators on Glioblastoma
Genes, Vol. 16, Pages 146: The Antidepressant Sertraline Modulates Gene Expression and Alternative Splicing Events in the Dermatophyte Trichophyton rubrum: A Comprehensive Analysis
Genes, Vol. 16, Pages 148: Impact of UV-Irradiated Mesoporous Titania Nanoparticles (mTiNPs) on Key Onco- and Tumor Suppressor microRNAs of PC3 Prostate Cancer Cells
Genes, Vol. 16, Pages 160: Evaluation of Pan-Cancer Immune Heterogeneity Based on DNA Methylation
Exploring metabolic reprogramming in esophageal cancer: the role of key enzymes in glucose, amino acid, and nucleotide pathways and targeted therapies
ITGA3 promotes pancreatic cancer progression through HIF1α- and c-Myc-driven glycolysis in a collagen I-dependent autocrine manner
<i>PIK3CA</i> mutation fortifies molecular determinants for immune signaling in vascular cancers

llm_spatial_and temporal_data_analysis

Modeling gene interactions in polygenic prediction via geometric deep learning [METHODS]
Estimating fruit tree growth curves in breeding field using fragmented longitudinal data: An application to citrus hybrid seedlings
Simulation and quantitative analysis of spatial centromere distributionpatterns
TIME-CoExpress: Temporal Trajectory Modeling of Dynamic Gene Co-expression Patterns Using Single-Cell Transcriptomics Data
Bayesian inference of fitness landscapes via tree-structured branching processes
SpaTM: Topic Models for Inferring Spatially Informed Transcriptional Programs
SVCROWS: A User-Defined Tool for Delineating Biologically Significant Structural Variants in Heterogeneous Datasets
SpaIM: Single-cell Spatial Transcriptomics Imputation via Style Transfer
Fast tumor phylogeny regression via tree-structured dual dynamic programming
Multi-species integration, alignment and annotation of single-cell RNA-seq data with CAMEX
Reproducible Boolean model analyses and simulations with the CoLoMoTo software suite: a tutorial.
Phylo-HS: A phylogenetic hierarchical softmax for taxonomic classification
SimdMinimizers: Computing random minimizers, fast
Untying Rates of Gene Gain and Loss Leads to a New Phylogenetic Approach
Tracing human trait evolution through integrative genomics and temporal annotations
DeST-OT: Alignment of spatiotemporal transcriptomics data
Epigenetic ageing clocks: statistical methods and emerging computational challenges

llm_molecular_pathways_and gene_regulation_in_plants

High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration [RESOURCES]
ERGA-BGE genome of Androsace saussurei Dentant, Lavergne, F. C. Boucher & S. Ibanez, a recently described plant from the rooftops of Europe
Genes, Vol. 16, Pages 79: Research Progress on Gene Regulation of Plant Floral Organogenesis
Genes, Vol. 16, Pages 97: Identification and Functional Analysis of Candidate Genes Influencing Citrus Leaf Size Through Transcriptome and Coexpression Network Approaches
Genes, Vol. 16, Pages 124: Does Asymmetric Reproductive Isolation Predict the Direction of Introgression in Plants?
Genes, Vol. 16, Pages 127: Genome-Wide Identification and Characterization of Histone Acetyltransferases and Deacetylases in Cucumber, and Their Implication in Developmental Processes
Genes, Vol. 16, Pages 132: Transcriptomic Profiling Highlights Metabolic and Biosynthetic Pathways Involved in In Vitro Flowering in Anoectochilus roxburghii (Wall.) Lindl.
Genes, Vol. 16, Pages 143: Decoding the Dialog Between Plants and Arbuscular Mycorrhizal Fungi: A Molecular Genetic Perspective
Genes, Vol. 16, Pages 152: ECE-CYC1 Transcription Factor CmCYC1a May Interact with CmCYC2 in Regulating Flower Symmetry and Stamen Development in Chrysanthemum morifolium
Fresh from the biotech pipeline: FDA approvals settle in 2024, but what next?
Functional innovation through new genes as a general evolutionary process

llm_biomedical_applications and_drug_discovery

Artificial intelligence and machine learning in cell-free-DNA-based diagnostics [REVIEW]
Revisiting the cancer microbiome using PRISM
Expanding Chemical Space: Developing a Compound Generative Pre-trained Transformer for De Novo Drug Design
Met-ID: An Open-Source Software for Comprehensive Annotation of Multiple On-Tissue Chemical Modifications in MALDI-MSI
mzLearn, a data-driven LC/MS signal detection algorithm, enables pre-trained generative models for untargeted metabolomics
Systems-level immunomonitoring in children with solid tumors to enable precision medicine
Spatial metabolomics to unravel cellular metabolism
A human metabolic map of pharmacological perturbations reveals drug modes of action
Quantum-computing-enhanced algorithm unveils potential KRAS inhibitors
A platform for the biomedical application of large language models

llm_single_cell gene_regulatory_networks

Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution [RESOURCES]
Improving the generalization of protein expression models with mechanistic sequence information
Digital Reprogramming Decodes Epigenetic Barriers of Cell Fate Changes
scGraphETM: Graph-Based Deep Learning Approach for Unraveling Cell Type-Specific Gene Regulatory Networks from Single-Cell Multi-Omics Data
Refining the cis-regulatory grammar learned by sequence-to-activity models by increasing model resolution
Predicting gene expression using millions of yeastpromoters reveals cis-regulatory logic
Building Foundation Models to Characterize Cellular Interactions via Geometric Self-Supervised Learning on Spatial Genomics
Integrating AlphaFold2 Models and Clinical Data to Improve the Assessment of Short Linear Motifs (SLiMs) and Their Variants' Pathogenicity
Refinement Strategies for Tangram for Reliable Single-Cell to Spatial Mapping
Genes, Vol. 16, Pages 101: Further Development of SAMPDI-3D: A Machine Learning Method for Predicting Binding Free Energy Changes Caused by Mutations in Either Protein or DNA

llm_rna regulation_and_function

Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y [RESEARCH]
Transcriptome-scale analysis uncovers conserved residues in the hydrophobic core of the bacterial RNA chaperone Hfq required for small regulatory RNA stability
Editor's Note on ‘MicroRNA-296 is enriched in cancer cells and downregulates p21WAF1 mRNA expression via interaction with its 3′ untranslated region’
Identification of Two Elusive Human Ribonuclease MRP-Specific Protein Components
Comprehensive Mapping of Human dsRNAome Reveals Conservation, Neuronal Enrichment, and Intermolecular Interactions
Class-agnostic annotation of small RNAs balances sensitivity and specificity in diverse organisms
URAdime - a tool for analyzing primer sequences in sequencing data to identify dimers and super-amplicons.
MUSICiAn: Genome-wide Identification of Genes Involved in DNA Repair via Control-Free Mutational Spectra Analysis
Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration
Genes, Vol. 16, Pages 77: ADAR Therapeutics as a New Tool for Personalized Medicine
Genes, Vol. 16, Pages 140: Landscape of Noncoding RNA in the Hypoxic Tumor Microenvironment
Genes, Vol. 16, Pages 162: Differential Expression of tRNA-Derived Small RNA Markers of Antidepressant Response and Functional Forecast of Duloxetine in MDD Patients
Beyond housekeeping: a new role of snoRNA in nascent protein secretion
Adapting to improve the author experience
Diversity and consequences of structural variation in the human genome
Cytoplasmic mRNA decay and quality control machineries in eukaryotes

llm_genetic disease_variant_sequencing

The rate and spectrum of new mutations in mice inferred by long-read sequencing [RESEARCH]
Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging [RESEARCH]
Who am I? Optimal Tissue for Germline Genetic Testing Post-Stem Cell Transplantation
Inhibition of cathepsin B blocks amyloidogenesis in the mouse models of neurological lysosomal diseases mucopolysaccharidosis type IIIC and sialidosis
A high-quality reference genome for the Ural Owl (Strix uralensis) enables investigations of cell cultures as a genomic resource for endangered species
Drug-Resistance Biomarkers in Leishmania infantum through Nanopore-Based Detection of Aneuploidy and Gene Copy Number Variations with LeishGenApp
Comprehensive mutational characterization of the calcium-sensing STIM1 EF-hand reveals residues essential for structure and function
Pooled long-read sequencing for structural variant characterization in schistosome populations
Clinical performance evaluation of a tiling amplicon panel for whole genome sequencing of respiratory syncytial virus
Human adult neurogenesis loss corresponds with cognitive decline during epilepsy progression
Long somatic DNA-repeat expansion drives neurodegeneration in Huntington’s disease
Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders
Genes, Vol. 16, Pages 74: Hypertrophic Cardiomyopathy: New Clinical and Therapeutic Perspectives of an &ldquo;Old&rdquo; Genetic Myocardial Disease
Genes, Vol. 16, Pages 92: The Prevalence and Clinical Characteristics of MYO3A-Associated Hearing Loss in 15,684 Hearing Loss Patients
Genes, Vol. 16, Pages 115: APCAD Part 2: A Novel Method for Detection of Meiotic Aneuploidy in Preimplantation Embryos
Genes, Vol. 16, Pages 116: Auditory Neuropathy Caused by a Structural Variation in the OTOF Gene, Identified Using Oxford Nanopore Adaptive Sampling
Genes, Vol. 16, Pages 119: Enhancement of the Precision ID Mitochondrial DNA Whole Genome System for Challenging Unidentified Human Remains
Genes, Vol. 16, Pages 135: Genomic and Transcriptomic Approaches Advance the Diagnosis and Prognosis of Neurodegenerative Diseases
Genes, Vol. 16, Pages 144: A Double-Gene Metabarcoding Approach for the Authentication of Shrimp Surimi-Based Products
Genes, Vol. 16, Pages 149: Systematic Review: Fragile X Syndrome Across the Lifespan with a Focus on Genetics, Neurodevelopmental, Behavioral and Psychiatric Associations
Genes, Vol. 16, Pages 151: Genetic Insights and Clinical Implications of NEU1 Mutations in Sialidosis
Genes, Vol. 16, Pages 161: NETest and Gastro-Entero-Pancreatic Neuroendocrine Tumors: Still Far from Routine Clinical Application? A Systematic Review
Genes, Vol. 16, Pages 169: Analysis of Short Tandem Repeat Expansions in a Cohort of 12,496 Exomes from Patients with Neurological Diseases Reveals Variable Genotyping Rate Dependent on Exome Capture Kits
Ion channel traffic jams: the significance of trafficking deficiency in long QT syndrome
Identifying novel response markers for spinal muscular atrophy revealed by targeted proteomics following gene therapy
In vivo CRISPR–Cas9 genome editing in mice identifies genetic modifiers of somatic CAG repeat instability in Huntington’s disease
Defining genes and pathways that modify huntingtin CAG repeat somatic instability in vivo
Population-based, first-tier genomic newborn screening in the maternity ward

llm_genome_evolution and_chromosome_structure

Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths [RESEARCH]
Fusion, fission, and scrambling of the bilaterian genome in Bryozoa [RESEARCH]
Distinct Genetic Populations and Resistance Backgrounds of the Malaria Vector Anopheles funestus in Tanzania
Exploring the role of transposable elements to sex gap in longevity in Drosophila species
Germline-restricted chromosome of songbirds has different centromere compared to regular chromosomes
Genes, Vol. 16, Pages 106: Origin and Genealogy of Rare mtDNA Haplotypes Detected in the Serbian Population
Genes, Vol. 16, Pages 86: Cytogenomics of Frieseomelitta varia (Hymenoptera: Apidae) and the Sharing of a Satellite DNA Family in Several Neotropical Meliponini Genera
Genes, Vol. 16, Pages 111: Phylogenetic and Codon Usage Bias Analysis Based on mt-DNA of Cyphochilus crataceus (Coleoptera: Melolonthinae) and Its Neighboring Species

llm_gene deletions_and_mutations

ISWI1 complex proteins facilitate developmental genome editing in Paramecium [RESEARCH]
VPS13D mutations disrupt mitochondrial homeostasis and locomotion in Caenorhabditis elegans
Synergistic effects of Ret coding and enhancer loss-of-function alleles cause progressive loss of inhibitory motor neurons in the enteric nervous system
Generation of iPSC-derived human venous endothelial cells for the modeling of vascular malformations and drug discovery
SMC motor proteins extrude DNA asymmetrically and can switch directions
Genes, Vol. 16, Pages 72: 22q11.21 Deletions: A Review on the Interval Mediated by Low-Copy Repeats C and D
Genes, Vol. 16, Pages 76: Compound Heterozygous p.(R124C) (Classic Lattice Corneal Dystrophy) and p.(R124H) (Granular Corneal Dystrophy Type 2) in TGFBI: Phenotype, Genotype, and Treatment
Genes, Vol. 16, Pages 80: Chromosome 4 Duplication Associated with Strabismus Leads to Gene Expression Changes in iPSC-Derived Cortical Neurons
Genes, Vol. 16, Pages 110: The Role of the MTUS1 Gene in the Development of Left Ventricular Noncompaction Cardiomyopathy&mdash;A Case Report
Genes, Vol. 16, Pages 117: Ecological Trait Differences Are Associated with Gene Expression in the Primary Visual Cortex of Primates
Genes, Vol. 16, Pages 123: Prevalence and Clinical Characteristics of OTOGL-Associated Hearing Loss Identified in a Cohort of 7065 Japanese Patients with Hearing Loss
Genes, Vol. 16, Pages 129: Cochlear Implant Challenges in Children with Ichthyosis: A Systematic Review
Genes, Vol. 16, Pages 142: Differentially Expressed Genes in Cardiomyocytes of the First Camelized Mouse Model, Nrapc.255ins78 Mouse
Genes, Vol. 16, Pages 154: Genetic Overlap of Thoracic Aortic Aneurysms and Intracranial Aneurysms

llm_stem_cell engineering_and_therapy

AAV vector transduction restriction and attenuated toxicity in hESCs via a rationally designed inverted terminal repeat
Single-cell DNA sequencing reveals pervasive positive selection throughout preleukemic evolution
BCL11A +58/+55 enhancer-editing facilitates HSPC engraftment and HbF induction in rhesus macaques conditioned with a CD45 antibody-drug conjugate
Gene editing without ex vivo culture evades genotoxicity in human hematopoietic stem cells
Different effects of fatty acid oxidation on hematopoietic stem cells based on age and diet
Maturation and persistence of CAR T cells derived from human pluripotent stem cells via chemical inhibition of G9a/GLP
Modeling early gastrulation in human blastoids with DNA methylation patterns of natural blastocysts
Adult bi-paternal offspring generated through direct modification of imprinted genes in mammals
Genes, Vol. 16, Pages 134: Trophectoderm Biopsy: Present State of the Art
Generation of live mice from haploid ESCs with germline-DMR deletions or switch
Conversion of placental hemogenic endothelial cells to hematopoietic stem and progenitor cells
Battling Diamond-Blackfan anaemia
Pricey sickle cell gene therapies primed for change
Generating allogeneic CAR-NKT cells for off-the-shelf cancer immunotherapy with genetically engineered HSP cells and feeder-free differentiation culture

llm_molecular function_and_modification

Proximity-activated guide RNA of CRISPR–Cas12a for programmable diagnostic detection and gene regulation
DNA end sensing and cleavage by the Shedu anti-phage defense system
Molecular basis of proton sensing by G protein-coupled receptors
Rational multienzyme architecture design with iMARS
Genes, Vol. 16, Pages 107: Gene Therapy and Diabetes: A Narrative Review of Recent Advances and the Role of Multidisciplinary Healthcare Teams
Has_circ_ASH1L acts as a sponge for miR-1254 to promote the malignant progression of cervical cancer by targeting CD36
CRISPR knock-in of a chimeric antigen receptor into <i>GAPDH</i> 3’UTR locus generates potent B7H3-specific NK-92MI cells
Apaf-1 is an evolutionarily conserved DNA sensor that switches the cell fate between apoptosis and inflammation
Structural insights into the agonist activity of the nonpeptide modulator JR14a on C3aR
Chemogenetics for sensing antigens
Enantioselective reductive cross-couplings to forge C(sp<sup>2</sup>)–C(sp<sup>3</sup>) bonds by merging electrochemistry with nickel catalysis
Structure and function of a near fully-activated intermediate GPCR-Gαβγ complex
The therapeutic potential of circular RNAs
Frequency locked whispering evanescent resonator (FLOWER) for biochemical sensing applications

llm_research corrections_and_retractions

Correction to ‘DNA target binding-induced pre-crRNA processing in type II and V CRISPR-Cas systems’
Correction to ‘ECBD: European chemical biology database’
Retraction Note: Circular RNA hsa_circ_0009172 suppresses gastric cancer by regulation of microRNA-485-3p-mediated NTRK3
Author Correction: Heat acclimation in mice requires preoptic BDNF neurons and postsynaptic potentiation
Correction: RapaCaspase-9-based suicide gene applied to the safety of IL-1RAP CAR-T cells
Correction: The disparate burden of infectious diseases
Retraction Note: Tumour microenvironment programming by an RNA–RNA-binding protein complex creates a druggable vulnerability in IDH-wild-type glioblastoma
Author Correction: A multilineage screen identifies actionable synthetic lethal interactions in human cancers
Author Correction: The ZmCPK39–ZmDi19–ZmPR10 immune module regulates quantitative resistance to multiple foliar diseases in maize
Author Correction: Burdens of type 2 diabetes and cardiovascular disease attributable to sugar-sweetened beverages in 184 countries
Author Correction: A comprehensive human embryo reference tool using single-cell RNA-sequencing data

llm_genomic_studies_of_disease

methylGrapher: genome-graph-based processing of DNA methylation data from whole genome bisulfite sequencing
Cell type-specific eQTL detection from single-cell RNA-seq reveals post-transcriptional regulatory mechanisms in human islets
Causal modeling of gene effects from regulators to programs to traits: integration of genetic associations and Perturb-seq
MeQTL Mapping in African American Hepatocytes Reveals Shared Genetic Regulators of DNA Methylation and Gene Expression
Cross cell-type systems genetics reveals the influence of eQTL at multiple points in the developmental trajectory of mouse neural progenitor cells
Genetic mapping of serum metabolome to chronic diseases among Han Chinese
Trans-ancestry genome-wide study of depression identifies 697 associations implicating cell types and pharmacotherapies
Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Genes, Vol. 16, Pages 84: Missing Regulation Between Genetic Association and Transcriptional Abundance for Hypercholesterolemia Genes
Genes, Vol. 16, Pages 98: Research Progress and Clinical Translation Potential of Coronary Atherosclerosis Diagnostic Markers from a Genomic Perspective
Genes, Vol. 16, Pages 118: Editorial for the Bioinformatics of Human Diseases Special Issue
Genes, Vol. 16, Pages 157: Causal Associations Between Remnant Cholesterol Levels and Atherosclerosis-Related Cardiometabolic Risk Factors: A Bidirectional Mendelian Randomization Analysis
Genes, Vol. 16, Pages 165: Col5a3 Likely Promotes Adipogenesis of 3T3-L1 Through Oxidative Phosphorylation
Half of land use carbon emissions in Southeast Asia can be mitigated through peat swamp forest and mangrove conservation and restoration
Multiomics reveals that triacylglycerol mobilization helps drive recovery from mitochondrial stress
Overcoming challenges associated with broad sharing of human genomic data
Long-term liver outcomes after metabolic surgery in compensated cirrhosis due to metabolic dysfunction-associated steatohepatitis

llm_mitochondrial mutations_and_disease

Limited genetic diversity among Malassezia furfur isolates during two one-year neonatal and pediatric bloodstream infection surveys confirms preference for one specific IGS1 genotype in deep-seated infections
Development of metagenomic methods for non-invasive health monitoring of endangered species: Unveiling hidden microbial threats in fecal samples
Genomic characterisation of Listeria monocytogenes isolated from normally sterile human body fluids in Lithuania from 2016 to 2021
Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom
Genes, Vol. 16, Pages 108: Atypical Leber Hereditary Optic Neuropathy (LHON) Associated with a Novel MT-CYB:m.15309T&gt;C(Ile188Thr) Variant

llm_gene_identification under_stress_conditions

Bulk segregant analysis reveals genomic regions associated with imidacloprid resistance in the Colorado potato beetle
A Recessive oca2 Mutation Underlies Albinism in Xiphophorus fish
Identification of QTL for reproductive success under heat stress conditions through a tomato MAGIC population
XDH-1 inactivation causes xanthine stone formation in C. elegans which is inhibited by SULP-4-mediated anion exchange in the excretory cell
GO Big or Go Home: A New Gene Ontology Subset that Improves Plant Gene Function Prediction
A natural variant of COOL1 gene enhances cold tolerance for high-latitude adaptation in maize
Genes, Vol. 16, Pages 105: Transcriptome Reveals the Differential Regulation of Sugar Metabolism to Saline&ndash;Alkali Stress in Different Resistant Oats
Genes, Vol. 16, Pages 109: Genome-Wide Identification and Characterization of the CDPK Family of Genes and Their Response to High-Calcium Stress in Yinshania henryi
Genes, Vol. 16, Pages 90: Comparison and Classification of LMW-GS Genes at Glu-3 Loci of Common Wheat
Genes, Vol. 16, Pages 96: Construction of a High-Density Genetic Linkage Map and QTL Mapping for Stem Rot Resistance in Passion Fruit (Passiflora edulis Sims)
Genes, Vol. 16, Pages 99: Genome-Wide Identification and Expression Analysis Under Abiotic Stress of the Lipoxygenase Gene Family in Maize (Zea mays)
Genes, Vol. 16, Pages 126: Integration of GWAS and Co-Expression Network Analysis Identified Main Genes Responsible for Nitrogen Uptake Traits in Seedling Waxy Corn
Genes, Vol. 16, Pages 130: The PLA Gene Family in Tomato: Identification, Phylogeny, and Functional Characterization
Genes, Vol. 16, Pages 137: Characterization of Metabolites and Transcriptome of Pepper Accessions from Four Southern Provinces of China
Genes, Vol. 16, Pages 141: The Prevalence of Single Nucleotide Polymorphisms of the AOC1 Gene Associated with Diamine Oxidase (DAO) Enzyme Deficiency in Healthy Newborns: A Prospective Population-Based Cohort Study
Genes, Vol. 16, Pages 145: Vacuolar (H+)-ATPase Genes Are Essential for Cuticle and Wing Development in Locusta migratoria
Genes, Vol. 16, Pages 155: Genome-Wide Identification and Characterization of the BZR Transcription Factor Gene Family in Leymus chinensis
Genes, Vol. 16, Pages 158: The GA2ox Gene Family in Solanum pennellii: Genome-Wide Identification and Expression Analysis Under Salinity Stresses
Genes, Vol. 16, Pages 166: The Potential Role of Brassica napus Metallothioneins in Salt Stress and Interactions with Plant Growth-Promoting Bacteria

llm_genome sequencing_and_analysis

Hybrid sequencing reveals the genome of a Chrysochromulina parva virus and highlight its distinct replication strategy
Transcriptome mining reveals diversity and evolution of iflaviruses in Lepidoptera
First genomic resource of Candidatus Phytoplasma pyri associated to pear decline
Assembly, Annotation, and Comparative Analysis of the Mitochondrial Genome of Winged Bean (Psophocarpus tetragonolobus): Insights into Evolutionary Adaptation and Codon Usage Bias
ERGA-BGE genome of Cheirolophus tagananensis: an IUCN endangered shrub endemic to the Canary Islands
Genome assembly of Bougainvillia cf. muscus (Cnidaria: Hydrozoa)
Genes, Vol. 16, Pages 87: Novel Reassortants of Oropouche Virus (OROV) Are Causing Maternal&ndash;Fetal Infection During Pregnancy, Stillbirth, Congenital Microcephaly and Malformation Syndromes
Genes, Vol. 16, Pages 88: Complete Mitochondrial Genome of King Threadfin, Polydactylus macrochir (G&uuml;nther, 1867): Genome Characterization and Phylogenetic Analysis
Genes, Vol. 16, Pages 121: Genome-Wide Identification and Characterization of the Pirin Gene Family in Nicotiana benthamiana

llm_cellular_responses to_stress_and_pathogens

Nucleoporins shape germ granule architecture and balance small RNA silencing pathways
Perception of a pathogenic signature initiates intergenerational protection
Genes, Vol. 16, Pages 100: History of Biological Databases, Their Importance, and Existence in Modern Scientific and Policy Context
Genes, Vol. 16, Pages 103: Arabidopsis thaliana DNA Damage Response Mutants Challenged with Genotoxic Agents&mdash;A Different Experimental Approach to Investigate the TDP1&alpha; and TDP1&beta; Genes
Genes, Vol. 16, Pages 78: The Impact of Storage Conditions on DNA Preservation in Human Skeletal Remains: A Comparison of Freshly Excavated Samples and Those Stored for 12 Years in a Museum Depot
Genes, Vol. 16, Pages 93: Oxidative-Stress-Mediated Epigenetic Dysregulation in Spermatogenesis: Implications for Male Infertility and Offspring Health
Genes, Vol. 16, Pages 94: Casein Kinase I Protein Hrr25 Is Required for Pin4 Phosphorylation and Mediates Cell Wall Integrity Signaling in Saccharomyces cerevisiae
Genes, Vol. 16, Pages 95: Hallmarks of DNA Damage Response in Germination Across Model and Crop Species
Indirect recognition of pathogen virulence proteins to activate plant immune receptors

llm_genetic_diversity and_population_structure_analysis

Evaluating genotyping strategies for a small managed population with simulation
The central limit theorem for the number of mutations in the genealogy of a sample from a large population
Genes, Vol. 16, Pages 102: Genomic Rewilding of Domestic Animals: The Role of Hybridization and Selection in Wolfdog Breeds
Genes, Vol. 16, Pages 73: Population Genetics of Haliotis discus hannai in China Inferred Through EST-SSR Markers
Genes, Vol. 16, Pages 81: Evaluation of Genetic Diversity and Identification of Cultivars in Spray-Type Chrysanthemum Based on SSR Markers
Genes, Vol. 16, Pages 83: Identifying Genetic Predisposition to Dozer Lamb Syndrome: A Semi-Lethal Muscle Weakness Disease in Sheep
Genes, Vol. 16, Pages 114: Comparative Study of Statistical Approaches and SNP Panels to Infer Distant Relationships in Forensic Genetics
Genes, Vol. 16, Pages 131: Comparative Analysis of Genomic and Pedigree-Based Approaches for Genetic Evaluation of Morphological Traits in Pura Raza Espa&ntilde;ola Horses
Genes, Vol. 16, Pages 159: Accuracy of Genomic Predictions for Resistance to Gastrointestinal Parasites in Australian Merino Sheep
Genes, Vol. 16, Pages 163: Genome-Wide Association Studies for Lactation Performance in Buffaloes
Genes, Vol. 16, Pages 168: Association of BMP15 and GDF9 Gene Polymorphisms with Litter Size in Hu Sheep

llm_cancer biomarkers_and_proteomics

Survival Reinforced Transfer Learning for Multicentric Proteomic Subtyping and Biomarker Discovery
Rprot-Vec: A deep learning approach for fast protein structure similarity calculation
Systematic Evaluation of Normalization Approaches in Tandem Mass Tag and Label-Free Protein Quantification Data Using PRONE
The human zinc-binding cysteine proteome
Hyperacute rejection-engineered oncolytic virus for interventional clinical trial in refractory cancer patients
High-resolution spatially resolved proteomics of complex tissues based on microfluidics and transfer learning
Comparative proteomic landscapes elucidate human preimplantation development and failure
Genes, Vol. 16, Pages 85: Integrative Analysis of Radiation-Induced Senescence-Associated Secretory Phenotype Factors in Kidney Cancer Progression
Genes, Vol. 16, Pages 150: Retinol-Binding Protein 4 as a Biomarker in Cancer: Insights from a Pan-Cancer Analysis of Expression, Immune Infiltration, and Methylation
Genes, Vol. 16, Pages 167: Editorial for the Special Issue: Bioinformatics and Computational Biology for Cancer Prediction and Prognosis
FBXO22 promotes HCC angiogenesis and metastasis via RPS5/AKT/HIF-1α/VEGF-A signaling axis
Emerging roles of exosomes in diagnosis, prognosis, and therapeutic potential in ovarian cancer: a comprehensive review
Stromal architecture and fibroblast subpopulations with opposing effects on outcomes in hepatocellular carcinoma
The non-canonical proteome: a novel contributor to cancer proliferation
The hidden diversity of tumours
PEPPI-MS: gel-based sample pre-fractionation for deep top-down and middle-down proteomics

llm_single_cell_spatial_omics

ASTRO: Automated Spatial Whole-Transcriptome RNA-Expression Workflow
Enhancing spatial omics resolution by pseudo-interstitial pixels inference
MOSHPIT: accessible, reproducible metagenome data science on the QIIME 2 framework
Spatiotemporal single-cell roadmap of human skin wound healing
Longitudinal single-cell profiles of lung regeneration after viral infection reveal persistent injury-associated cell states
Global organelle profiling reveals subcellular localization and remodeling at proteome scale
Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics
Profiling the total transcriptome of single nuclei in archived samples with snRandom-seq
Uniform volumetric single-cell processing for organ-scale molecular phenotyping
Human subcutaneous and visceral adipocyte atlases uncover classical and nonclassical adipocytes and depot-specific patterns
A genome-wide atlas of human cell morphology
The next generation of in situ multi-omics
Multiplexed spatial mapping of chromatin features, transcriptome and proteins in tissues
Author Correction: Resolving tissue complexity by multimodal spatial omics modeling with MISO
An accessible workflow for high-sensitivity proteomics using parallel accumulation–serial fragmentation (PASEF)

llm_viral_protein structure_and_function

Nucleocapsid assembly drives Ebola viral factory maturation and dispersion
Squeeze pumping of lipids and insecticides by ABCH transporter
Passage of the HIV capsid cracks the nuclear pore
Designed mosaic nanoparticles enhance cross-reactive immune responses in mice
Structural and functional analysis of the Nipah virus polymerase complex
Structure-guided discovery of viral proteins that inhibit host immunity
Assembly and architecture of endogenous NMDA receptors in adult cerebral cortex and hippocampus
Receptor binding, structure, and tissue tropism of cattle-infecting H5N1 avian influenza virus hemagglutinin
Structure of small HBV surface antigen reveals mechanism of dimer formation
Liver-avoiding capsids draw $1.1 billion
The Marburg virus outbreak is a critical moment for Rwanda’s one health policy

llm_protein_function and_cellular_processes

Norepinephrine-mediated slow vasomotion drives glymphatic clearance during sleep
Mechanisms of memory-supporting neuronal dynamics in hippocampal area CA3
Transport and inhibition mechanism for human TauT-mediated taurine uptake
Dynamic omniphobic surfaces enable the stable dropwise condensation of completely wetting refrigerants
Mitochondrial protein import stress
A temperature-inducible protein module for control of mammalian cell fate
Precision control of cellular functions with a temperature-sensitive protein
Photothermal nanofiber-mediated photoporation for gentle and efficient intracellular delivery of macromolecules

llm_genetic_variants and_disease_phenotypes

Genes, Vol. 16, Pages 91: Genotype&ndash;Phenotype Correlations of Nance&ndash;Horan Syndrome in Male and Female Carriers of a Novel Variant
Genes, Vol. 16, Pages 120: Novel TBR1 c.1303C&gt;T Variant Led to Diagnosis of Intellectual Developmental Disorder with Autism and Speech Delay: Application of Comprehensive Family-Based Whole-Genome Analysis
Genes, Vol. 16, Pages 122: Identification of Alterations in the Expression of Genes Related to the Implant Failure in Spanish Patients with Down Syndrome and Periodontal Disease
Genes, Vol. 16, Pages 125: MicroRNAs miR-148a-3p, miR-425-3p, and miR-20a-5p in Patients with IgA Nephropathy
Genes, Vol. 16, Pages 136: 16q24.3 Microdeletions Disrupting Upstream Non-Coding Region of ANKRD11 Cause KBG Syndrome
Genes, Vol. 16, Pages 147: Syndromic and Non-Syndromic Primary Failure of Tooth Eruption: A Genetic Overview
Genes, Vol. 16, Pages 171: The Relationship of the Pathogenic Variant rs721048 in the Intron of the EHBP1 Gene with the Development of Prostate Cancer and Colorectal Cancer in the Kazakh Population

llm_immune resistance_transcription_regulation

Rice transcription factor bHLH25 confers resistance to multiple diseases by sensing H<sub>2</sub>O<sub>2</sub>
H₂O₂ regulates rice defense via bHLH25 oxidation
Metabolite is a part of immune-regulating circuit

llm_novel_gene therapy_vectors_and_applications

Intracisternal vs intraventricular injection of AAV1 result in comparable, widespread transduction of the dog brain
AAV library screening identifies novel vector for efficient transduction of human aorta
Safety, efficacy, and immunogenicity of a novel IgG degrading enzyme (KJ103): results from two randomised, blinded, phase 1 clinical trials
Incomplete elimination of viral genomes is associated with chronic inflammation in nonhuman primate livers after AAV-mediated gene transfer
Co-delivery of IL-1Ra and SOX9 via AAV inhibits inflammation and promotes cartilage repair in surgically induced osteoarthritis animal models

arxiv_genetics

Unified meta regression models for rare variant association studies
R allele of ACTN3 R577X gene polymorphism is associated with Elite Indian Boxer Status

s_nat_protocols

A multifunctional sensor for cell traction force, matrix remodeling and biomechanical assays in self-assembled 3D tissues in vitro
Fabrication of nonplanar tapered fibers to integrate optical and electrical signals for neural interfaces in vivo
Fabrication of high-performance tin halide perovskite thin-film transistors via chemical solution-based composition engineering

s_nat_med

Intermittent fasting is good for losing (some) weight
An online multidomain lifestyle intervention to prevent cognitive decline in at-risk older adults: a randomized controlled trial
Estimating future heat-related and cold-related mortality under climate change, demographic and adaptation scenarios in 854 European cities
Phenome-wide associations of sleep characteristics in the Human Phenotype Project

s_nat_gen

Integrative proteogenomic analysis identifies COL6A3-derived endotrophin as a mediator of the effect of obesity on coronary artery disease

s_cell

Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation
Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution
Synthetic organizer cells guide development via spatial and biochemical instructions

s_nature_biotech

Mushroom makes tasty eco-asphalt

s_mdpi_genes

Genes, Vol. 16, Pages 164: The Association of Genetic Variants Within the Type XII Collagen and Tenascin C Genes with Knee Joint Laxity Measurements
Genes, Vol. 16, Pages 153: Effects of Physical Exercise on MuRF-1/TRIM63&nbsp;mRNA Expression in Humans: A Systematic Review
Genes, Vol. 16, Pages 139: Genetic Variants of SLC22A1 rs628031 and rs622342 and Glycemic Control in T2DM Patients from Northern Mexico
Genes, Vol. 16, Pages 113: Unravelling the Relationship Between Height, Lean Mass, Alzheimer&rsquo;s Disease and Cognition Through Mendelian Randomization
Genes, Vol. 16, Pages 104: The Epigenetic Machinery and Energy Expenditure: A Network to Be Revealed
Genes, Vol. 16, Pages 82: Hereditary Breast Cancer: Comprehensive Risk Assessment and Prevention Strategies

s_nat_comm

On the giant deformation and ferroelectricity of guanidinium nitrate
3D N-heterocyclic covalent organic frameworks for urea photosynthesis from NH<sub>3</sub> and CO<sub>2</sub>

s_cell_stem

Pluripotent stem-cell-derived therapies in clinical trial: A 2025 update
Mouse totipotent blastomere-like cells model embryogenesis from zygotic genome activation to post implantation
Maternal gut microbiota influence stem cell function in offspring
Patient-derived glioblastoma organoids as real-time avatars for assessing responses to clinical CAR-T cell therapy

s_nature_cellbio

Tripotency in human pancreas